This is a classic photograph on a brisk winter morning, of what a flashing looks like when it's properly installed on a roof. Note how the shingle is cut at the right point, and the rubber gasket fits all the way around the LB pullpoint.
Also, you might notice how there's wire that is suspended, coming out of it. Those wires are held above the roof surface using zipties and tension on the groundwire. The code violation here is the tension being placed on the grounding conductor. The alternative? None was ever offered, and none was given. It might have been considered OK if we used a different wire to hang the other wires by its tension. As long as that particular wire wasn't a conductor of any kind. But that would just seem a bit odd, considering that we were already under certain time constraints, and it would also be a questionable use of additional copper.